bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
Traceback (most recent call last):
File "/apps/biobakery-workflows/3.0.0a7/bin/wmgx.py", line 184, in <module>
workflow.go()
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/workflow.py", line 800, in go
_runner.run_tasks(task_idxs)
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/runners.py", line 141, in run_tasks
self.ctx._handle_task_started(idx)
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/workflow.py", line 884, in _handle_task_started
self._reporter.task_started(task_no)
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 196, in task_started
r.task_started(task_no)
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 641, in task_started
self.log_event("ready and waiting for resources", task_no, self._daginfo(task_no))
File "/apps/biobakery-workflows/3.0.0a7/lib/python3.9/site-packages/anadama2/reporters.py", line 597, in _daginfo
return msg.format(len(parents), parents, len(children), children)
TypeError: object of type 'dict_keyiterator' has no len()
I don't know how to troubleshoot. Any direction, hint or idea would be welcome.
I couldn't find any related issues here, on the anadama2 github page or the biobakery forum
Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.
Dear developers, I'm trying to install on a HPC:
conda create -y -p ${TARGETDIR} -c conda-forge -c bioconda -c biobakery "biobakery_workflows=3.0.0a7"
kneaddata
databases withkneaddata_database
commandI tried to execute with the example data form this repository:
but always I get this error:
I don't know how to troubleshoot. Any direction, hint or idea would be welcome. I couldn't find any related issues here, on the anadama2 github page or the biobakery forum
Thanks